I had a similar experience with a Destiny 6100 security system. After meticulously wiring the system I/O to every sensor, I tried to "program" it. After it was clear that it would take many hours to do it via the system keypad, I ordered the adapter cable to connect it to the serial port of a PC. As your experience, the software was beyond cryptic (what GUI?). I'm convinced that this is done on purpose for job security and high profits to "authorized dealers" only. WKetel sounds like he could be "one of them" - I dismiss the "evil tampering" argument as bull****! I also think that Microsoft and their feature-overloaded bloatware is that way for similar reasons. Whatever happened to simple elegance?

Updating a design costs money, and in addition, if I want a replacement for something that has worked well, I may not want to find a bunch of changes have been added. After all, the functionality of an alarm system that is needed has not changed. One more thing, which is that if the original system was that complex, those who have mastered it would probably not be very happy to find that it has changed, and everything that they learned is now obsolete. After all, alarm systems come under the heading of durable goods, meaning that they are not intended to be replaced every six months to keep up with the latest fads. Aside from that, it is definitely in the installers interest to have the system programming so complex that the users would not be able to change anything, since this assures that there will be service calls in the future in order to make changes. Also, the complexity tends to keep those who would tamper with the system for "evil" purposes a bit less likely to be able to do it conveniently.

Funny, when my first home alarm system was installed, I marveled at the skill of the installer, who had to hide lots of sensor wires within the drywall or baseboard seams.
My second and current alarm system was all wireless, but still "old" technology from my perspective. The user interface for the controller is ancient -- the kind of stuff students might have done as a school project 15 or 20 years ago.
I don't keep up on this segment of the industry, and I'm sure there's much better equipment than what I have, but I think part of the problem is the service model. The home alarm industry has mostly copied the cell phone model -- sign up for monitoring service, and the equipment is either free or really cheap.
I think there's quite an opportunity there for differentiation.

Nice article. As an engineer myself developing alarm systems here in Malaysia, your experience serves me as a guideline not to piss off the end users.
By the way, was it lighting or lightning that fried the I/O lines?